The Dead Sea is located in the Dead Sea Rift, that is part of a long fissure in the Earth's surface called the Great Rift Valley. The 6000 km (3700 mile) long Great Rift Valley extends from the Taurus Mountains of Turkey to the Zambezi Valley in southern Africa. The Great Rift Valley formed in Miocene times as a result of the Arabian Plate moving northward and then eastward away from the African Plate.

Around three million years ago what is now the valley of the Jordan River, Dead Sea, and Wadi Arabah/Nahal Arava was repeatedly inundated by waters from the Mediterranean Sea. The waters formed in a narrow, crooked bay which was connected to the sea through what is now the Jezreel Valley. The lake that occupied the Dead Sea Rift, named "Lake Sodom", deposited beds of salt, eventually coming to be 3 km (2 miles) thick.

According to geological theory, approximately two million years ago the land between the Rift Valley and the Mediterranean Sea rose to such an extent that the ocean could no longer flood the area. Thus, the long bay became a long lake.The Jordan River is the only major stream flowing into Dead Sea. There are no outlet streams.